scikit-network 0.33.0__cp312-cp312-macosx_10_9_x86_64.whl

scikit_network-0.33.0.dist-info/RECORD

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scikit_network-0.33.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (70.3.0)
+Root-Is-Purelib: false
+Tag: cp312-cp312-macosx_10_9_x86_64
+

scikit_network-0.33.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+sknetwork

sknetwork/__init__.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""Top-level package for scikit-network"""
+
+__author__ = """scikit-network team"""
+__email__ = "thomas.bonald@telecom-paris.fr"
+__version__ = '0.33.0'
+
+import sknetwork.topology
+import sknetwork.path
+import sknetwork.classification
+import sknetwork.clustering
+import sknetwork.embedding
+import sknetwork.hierarchy
+import sknetwork.linalg
+import sknetwork.linkpred
+import sknetwork.ranking
+import sknetwork.data
+import sknetwork.utils
+import sknetwork.visualization
+import sknetwork.gnn

sknetwork/base.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created in June 2019
+@author: Quentin Lutz <qlutz@enst.fr>
+"""
+import inspect
+
+
+class Algorithm:
+    """Base class for all algorithms.
+    """
+    def get_params(self):
+        """Get parameters as dictionary.
+
+        Returns
+        -------
+        params : dict
+            Parameters of the algorithm.
+        """
+        signature = inspect.signature(self.__class__.__init__)
+        params_exclude = ['self', 'random_state', 'verbose']
+        params = dict()
+        for param in signature.parameters.values():
+            name = param.name
+            if name not in params_exclude:
+                try:
+                    value = self.__dict__[name]
+                except KeyError:
+                    continue
+                params[name] = value
+        return params
+
+    def set_params(self, params: dict) -> 'Algorithm':
+        """Set parameters of the algorithm.
+
+        Parameters
+        ----------
+        params : dict
+            Parameters of the algorithm.
+
+        Returns
+        -------
+        self : :class:`Algorithm`
+        """
+        valid_params = self.get_params()
+        if type(params) is not dict:
+            raise ValueError('The parameters must be given as a dictionary.')
+        for name, value in params.items():
+            if name not in valid_params:
+                raise ValueError(f'Invalid parameter: {name}.')
+            setattr(self, name, value)
+        return self
+
+    def __repr__(self):
+        params_string = []
+        for name, value in self.get_params().items():
+            if type(value) == str:
+                value = "'" + value + "'"
+            else:
+                value = str(value)
+            params_string.append(name + '=' + value)
+        return self.__class__.__name__ + '(' + ', '.join(params_string) + ')'
+
+    def fit(self, *args, **kwargs):
+        """Fit algorithm to data."""
+        raise NotImplementedError

sknetwork/classification/__init__.py

@@ -0,0 +1,8 @@
+"""classification module"""
+from sknetwork.classification.base import BaseClassifier
+from sknetwork.classification.diffusion import DiffusionClassifier
+from sknetwork.classification.knn import NNClassifier
+from sknetwork.classification.metrics import get_accuracy_score, get_confusion_matrix, get_f1_score, get_f1_scores, \
+    get_average_f1_score
+from sknetwork.classification.pagerank import PageRankClassifier
+from sknetwork.classification.propagation import Propagation

sknetwork/classification/base.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created in November 2019
+@author: Nathan de Lara <nathan.delara@polytechnique.org>
+"""
+from abc import ABC
+
+import numpy as np
+from scipy import sparse
+
+from sknetwork.base import Algorithm
+
+
+class BaseClassifier(Algorithm, ABC):
+    """Base class for classifiers.
+
+    Attributes
+    ----------
+    bipartite : bool
+        If ``True``, the fitted graph is bipartite.
+    labels_ : np.ndarray, shape (n_labels,)
+        Labels of nodes.
+    probs_ : sparse.csr_matrix, shape (n_row, n_labels)
+        Probability distribution over labels (soft classification).
+    labels_row_ , labels_col_ : np.ndarray
+        Labels of rows and columns (for bipartite graphs).
+    probs_row_, probs_col_ : sparse.csr_matrix, shapes (n_row, n_labels) and (n_col, n_labels)
+        Probability distributions over labels for rows and columns (for bipartite graphs).
+    """
+
+    def __init__(self):
+        self.bipartite = None
+        self.labels_ = None
+        self.probs_ = None
+        self.labels_row_ = None
+        self.labels_col_ = None
+        self.probs_row_ = None
+        self.probs_col_ = None
+
+    def predict(self, columns: bool = False) -> np.ndarray:
+        """Return the labels predicted by the algorithm.
+
+        Parameters
+        ----------
+        columns : bool
+            If ``True``, return the prediction for columns.
+
+        Returns
+        -------
+        labels : np.ndarray
+            Labels.
+        """
+        if columns:
+            return self.labels_col_
+        return self.labels_
+
+    def fit_predict(self, *args, **kwargs) -> np.ndarray:
+        """Fit algorithm to the data and return the labels. Same parameters as the ``fit`` method.
+
+        Returns
+        -------
+        labels : np.ndarray
+            Labels.
+        """
+        self.fit(*args, **kwargs)
+        return self.predict()
+
+    def predict_proba(self, columns=False) -> np.ndarray:
+        """Return the probability distribution over labels as predicted by the algorithm.
+
+        Parameters
+        ----------
+        columns : bool
+            If ``True``, return the prediction for columns.
+
+        Returns
+        -------
+        probs : np.ndarray
+            Probability distribution over labels.
+        """
+        if columns:
+            return self.probs_col_.toarray()
+        return self.probs_.toarray()
+
+    def fit_predict_proba(self, *args, **kwargs) -> np.ndarray:
+        """Fit algorithm to the data and return the probability distribution over labels.
+        Same parameters as the ``fit`` method.
+
+        Returns
+        -------
+        probs : np.ndarray
+            Probability of each label.
+        """
+        self.fit(*args, **kwargs)
+        return self.predict_proba()
+
+    def transform(self, columns=False) -> sparse.csr_matrix:
+        """Return the probability distribution over labels in sparse format.
+
+        Parameters
+        ----------
+        columns : bool
+            If ``True``, return the prediction for columns.
+
+        Returns
+        -------
+        probs : sparse.csr_matrix
+            Probability distribution over labels.
+        """
+        if columns:
+            return self.probs_col_
+        return self.probs_
+
+    def fit_transform(self, *args, **kwargs) -> sparse.csr_matrix:
+        """Fit algorithm to the data and return the probability distribution over labels in sparse format.
+        Same parameters as the ``fit`` method.
+
+        Returns
+        -------
+        probs : sparse.csr_matrix
+            Probability distribution over labels.
+        """
+        self.fit(*args, **kwargs)
+        return self.transform()
+
+    def _split_vars(self, shape: tuple):
+        """Split variables for bipartite graphs."""
+        if self.bipartite:
+            n_row = shape[0]
+            self.labels_row_ = self.labels_[:n_row]
+            self.labels_col_ = self.labels_[n_row:]
+            self.labels_ = self.labels_row_
+            self.probs_row_ = self.probs_[:n_row]
+            self.probs_col_ = self.probs_[n_row:]
+            self.probs_ = self.probs_row_
+        else:
+            self.labels_row_ = self.labels_
+            self.labels_col_ = self.labels_
+            self.probs_row_ = self.probs_
+            self.probs_col_ = self.probs_
+        return self

sknetwork/classification/base_rank.py

@@ -0,0 +1,133 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created in March 2020
+@author: Nathan de Lara <nathan.delara@polytechnique.org>
+"""
+from functools import partial
+from multiprocessing import Pool
+from typing import Union, Optional
+
+import numpy as np
+from scipy import sparse
+
+from sknetwork.classification.base import BaseClassifier
+from sknetwork.linalg.normalizer import normalize
+from sknetwork.ranking.base import BaseRanking
+from sknetwork.utils.check import check_labels, check_n_jobs
+from sknetwork.utils.format import get_adjacency_values
+
+
+class RankClassifier(BaseClassifier):
+    """Generic class for ranking based classifiers.
+
+    Parameters
+    ----------
+    algorithm :
+        Which ranking algorithm to use.
+    n_jobs :
+        If positive, number of parallel jobs allowed (-1 means maximum number).
+        If ``None``, no parallel computations are made.
+
+    Attributes
+    ----------
+    labels_ : np.ndarray, shape (n_labels,)
+        Label of each node.
+    probs_ : sparse.csr_matrix, shape (n_row, n_labels)
+        Probability distribution over labels.
+    labels_row_, labels_col_ : np.ndarray
+        Labels of rows and columns, for bipartite graphs.
+    probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
+        Probability distributions over labels for rows and columns (for bipartite graphs).
+    """
+    def __init__(self, algorithm: BaseRanking, n_jobs: Optional[int] = None, verbose: bool = False):
+        super(RankClassifier, self).__init__()
+
+        self.algorithm = algorithm
+        self.n_jobs = check_n_jobs(n_jobs)
+        self.verbose = verbose
+
+    @staticmethod
+    def _process_labels(labels: np.ndarray) -> list:
+        """Make one-vs-all binary labels from labels.
+
+        Parameters
+        ----------
+        labels
+
+        Returns
+        -------
+        List of binary labels.
+        """
+        labels_all = []
+        labels_unique, _ = check_labels(labels)
+
+        for label in labels_unique:
+            labels_binary = np.array(labels == label).astype(int)
+            labels_all.append(labels_binary)
+
+        return labels_all
+
+    @staticmethod
+    def _process_scores(scores: np.ndarray) -> np.ndarray:
+        """Post-processing of the scores.
+
+        Parameters
+        ----------
+        scores
+            Matrix of scores, shape number of nodes x number of labels.
+
+        Returns
+        -------
+        scores : np.ndarray
+        """
+        return scores
+
+    def _split_vars(self, shape):
+        """Split the vector of labels and build membership matrix."""
+        n_row = shape[0]
+        self.labels_row_ = self.labels_[:n_row]
+        self.labels_col_ = self.labels_[n_row:]
+        self.labels_ = self.labels_row_
+        self.probs_row_ = self.probs_[:n_row]
+        self.probs_col_ = self.probs_[n_row:]
+        self.probs_ = self.probs_row_
+
+    def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], labels: Union[np.ndarray, dict] = None,
+            labels_row: Union[np.ndarray, dict] = None, labels_col: Union[np.ndarray, dict] = None) -> 'RankClassifier':
+        """Fit algorithm to data.
+
+        Parameters
+        ----------
+        input_matrix :
+            Adjacency matrix or biadjacency matrix of the graph.
+        labels :
+            Known labels (dictionary or array; negative values ignored).
+        labels_row, labels_col :
+            Known labels on rows and columns (for bipartite graphs).
+        Returns
+        -------
+        self: :class:`RankClassifier`
+        """
+        adjacency, seeds_labels, bipartite = get_adjacency_values(input_matrix, values=labels, values_row=labels_row,
+                                                                  values_col=labels_col)
+        seeds_labels = seeds_labels.astype(int)
+        labels_unique, n_classes = check_labels(seeds_labels)
+        seeds_all = self._process_labels(seeds_labels)
+        local_function = partial(self.algorithm.fit_predict, adjacency)
+        with Pool(self.n_jobs) as pool:
+            scores = np.array(pool.map(local_function, seeds_all))
+        scores = scores.T
+
+        scores = self._process_scores(scores)
+        scores = normalize(scores)
+
+        probs = sparse.coo_matrix(scores)
+        probs.col = labels_unique[probs.col]
+
+        labels = np.argmax(scores, axis=1)
+        self.labels_ = labels_unique[labels]
+        self.probs_ = sparse.csr_matrix(probs, shape=(adjacency.shape[0], np.max(seeds_labels) + 1))
+        self._split_vars(input_matrix.shape)
+
+        return self